public class RelatedIon extends Ion
Ion.IonType
Modifier and Type | Field and Description |
---|---|
static RelatedIon |
RELATED_C_1
Related ion for C.
|
static RelatedIon |
RELATED_C_2
Related ion for C.
|
static RelatedIon |
RELATED_D_1
Related ion for D.
|
static RelatedIon |
RELATED_E_1
Related ion for E.
|
static RelatedIon |
RELATED_F_1
Related ion for F.
|
static RelatedIon |
RELATED_H_1
Related ion for H (C4H5N2).
|
static RelatedIon |
RELATED_H_2
Related ion for H.
|
static RelatedIon |
RELATED_K_1
Related ion for K.
|
static RelatedIon |
RELATED_K_2
Related ion for K.
|
static RelatedIon |
RELATED_K_3
Related ion for K.
|
static RelatedIon |
RELATED_M_1
Related ion for M (C2H4S).
|
static RelatedIon |
RELATED_N_1
Related ion for N.
|
static RelatedIon |
RELATED_Q_1
Related ion for Q.
|
static RelatedIon |
RELATED_Q_2
Related ion for Q.
|
static RelatedIon |
RELATED_R_1
Related ion for R.
|
static RelatedIon |
RELATED_R_2
Related ion for R.
|
static RelatedIon |
RELATED_R_3
Related ion for R.
|
static RelatedIon |
RELATED_R_4
Related ion for R (C5H10N2O).
|
static RelatedIon |
RELATED_W_1
Related ion for W (C9H7N).
|
static RelatedIon |
RELATED_Y_1
Related ion for Y (C7H7O).
|
atomChain, theoreticMass, theoreticMass1, type
Constructor and Description |
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RelatedIon(AminoAcid aminoAcidTarget,
AtomChain atomChain,
int subType)
Constructor for a related ion.
|
RelatedIon(AminoAcid aminoAcidTarget,
AtomChain atomChain,
int subType,
boolean save)
Constructor for a related ion.
|
Modifier and Type | Method and Description |
---|---|
String |
getName()
Returns the name of the ion.
|
NeutralLoss[] |
getNeutralLosses()
Returns the possible neutral losses of this ion type.
|
static int[] |
getPossibleSubtypes()
Returns the possible subtypes.
|
CvTerm |
getPrideCvTerm()
Returns the CV term adapted to the fragment ion.
|
CvTerm |
getPsiMsCvTerm()
Returns the CV term adapted to the fragment ion.
|
static ArrayList<RelatedIon> |
getRelatedIons(AminoAcid aminoAcidTarget)
Returns the list of related ions for the given amino acid.
|
static ArrayList<RelatedIon> |
getRelatedIons(char aa)
Returns the list of related ions for the given amino acid.
|
int |
getSubType()
Returns the ion subtype.
|
String |
getSubTypeAsString()
Returns the subtype as string.
|
boolean |
isSameAs(Ion anotherIon)
Returns a boolean indicating whether the ion is the same as another ion.
|
boolean |
isSameAs(RelatedIon anotherRelatedIon)
Compares the current related ion with another one based on their
composition.
|
getAtomicComposition, getGenericIon, getGenericIon, getImplementedIonTypes, getNeutralLossesAsString, getNeutralLossesAsString, getPossibleSubtypes, getPossibleSubtypesAsSet, getTheoreticMass, getTheoreticMz, getType, getTypeAsString, getTypeAsString, hasNeutralLosses, setAtomicComposition, setTheoreticMass
addUrParam, asLong, clearParametersMap, getUrParam, getUrParams, removeUrParam, setUrParams
getFirstLevel, getId, setFirstLevel, setId
jdoZooEvict, jdoZooGetBackup, jdoZooGetClassDef, jdoZooGetContext, jdoZooGetNode, jdoZooGetOid, jdoZooGetTimestamp, jdoZooHasState, jdoZooInit, jdoZooIsDeleted, jdoZooIsDetached, jdoZooIsDirty, jdoZooIsNew, jdoZooIsPersistent, jdoZooIsStateHollow, jdoZooIsTransactional, jdoZooMarkClean, jdoZooMarkDeleted, jdoZooMarkDetached, jdoZooMarkDirty, jdoZooMarkHollow, jdoZooMarkTransient, jdoZooSetOid, jdoZooSetTimestamp, toString, zooActivateRead, zooActivateWrite, zooActivateWrite
public static final RelatedIon RELATED_R_1
public static final RelatedIon RELATED_R_2
public static final RelatedIon RELATED_R_3
public static final RelatedIon RELATED_R_4
public static final RelatedIon RELATED_N_1
public static final RelatedIon RELATED_D_1
public static final RelatedIon RELATED_C_1
public static final RelatedIon RELATED_C_2
public static final RelatedIon RELATED_E_1
public static final RelatedIon RELATED_Q_1
public static final RelatedIon RELATED_Q_2
public static final RelatedIon RELATED_H_1
public static final RelatedIon RELATED_H_2
public static final RelatedIon RELATED_K_1
public static final RelatedIon RELATED_K_2
public static final RelatedIon RELATED_K_3
public static final RelatedIon RELATED_M_1
public static final RelatedIon RELATED_F_1
public static final RelatedIon RELATED_W_1
public static final RelatedIon RELATED_Y_1
public RelatedIon(AminoAcid aminoAcidTarget, AtomChain atomChain, int subType)
aminoAcidTarget
- the amino acid targetatomChain
- the atomic composition of this ionsubType
- the ion subtypepublic RelatedIon(AminoAcid aminoAcidTarget, AtomChain atomChain, int subType, boolean save)
aminoAcidTarget
- the amino acid targetatomChain
- the atomic composition of this ionsubType
- the ion subtypesave
- if true the related ion will be saved in the static map for
later reusepublic static ArrayList<RelatedIon> getRelatedIons(char aa)
aa
- the amino acid target single letter codepublic static ArrayList<RelatedIon> getRelatedIons(AminoAcid aminoAcidTarget)
aminoAcidTarget
- the amino acid targetpublic String getName()
Ion
public CvTerm getPrideCvTerm()
Ion
getPrideCvTerm
in class Ion
public CvTerm getPsiMsCvTerm()
Ion
getPsiMsCvTerm
in class Ion
public boolean isSameAs(RelatedIon anotherRelatedIon)
anotherRelatedIon
- the other related ionpublic int getSubType()
Ion
getSubType
in class Ion
public String getSubTypeAsString()
Ion
getSubTypeAsString
in class Ion
public static int[] getPossibleSubtypes()
public NeutralLoss[] getNeutralLosses()
Ion
getNeutralLosses
in class Ion
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